OOIR: Observatory of International Research

Papers

(The median citation count of Journal of Molecular Evolution is 2. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 250 papers]. The publications cover those that have been published in the past four years, i.e., from 2022-01-01 to 2026-01-01.)

Article	Citations
Correction: Stochastic Epigenetic Modification and Evolution of Sex Determination in Vertebrates	52
Molecular Evolution of Malacostracan Short Wavelength Sensitive Opsins	36
Correction: Analysis of Cancer-Resisting Evolutionary Adaptations in Wild Animals and Applications for Human Oncology	36
Modified Metabolism and Response to UV Radiation: Gene Expression Variations Along an Elevational Gradient in the Asiatic Toad (Bufo gargarizans)	33
Extant Sequence Reconstruction: The Accuracy of Ancestral Sequence Reconstructions Evaluated by Extant Sequence Cross-Validation	30
Molecular Evolution of the Green-Sensitive Opsins (RH2) in Sulawesi Oryzias Species with a Single Origin	24
Prebiotic N-(2-Aminoethyl)-Glycine (AEG)-Assisted Synthesis of Proto-RNA?	22
Avoiding Catastrophic Mutations Accurately Predicts Amino Acid to Codon Pairing	21
Scaling up Functional Analyses of the G Protein-Coupled Receptor Rhodopsin	19
Embracing Complexity: Yeast Evolution Experiments Featuring Standing Genetic Variation	17
Unusual Evolution of Cephalopod Tryptophan Indole-Lyases	17
Screening for Viruses in Pallas’s Long-Tongued Bats (Glossophaga soricina) in Brazil	16
The Ancient Origins of Death Domains Support the ‘Original Sin’ Hypothesis for the Evolution of Programmed Cell Death	14
Evaluating Pretrained Protein Language Model Embeddings as Proxies for Functional Similarity	13
Overlaps Between CDS Regions of Protein-Coding Genes in the Human Genome: A Case Study on the NR1D1-THRA Gene Pair	13
Odorant-Binding and Chemosensory Proteins in Fig Wasps: Evolutionary Insights From Comparative Studies	13
Post-Subfunctionalization Functions of HIF-1αA and HIF-1αB in Cyprinid Fish: Fine-Tuning Mitophagy and Apoptosis Regulation Under Hypoxic Stress	13
An Ultimate Question for Functional A-to-I mRNA Editing: Why Not a Genomic G?	13
Learning from the Codon Table: Convergent Recoding Provides Novel Understanding on the Evolution of A-to-I RNA Editing	13
MEGA 12.1: Cross-Platform Release for macOS and Linux Operating Systems	12
Organophosphorus Compound Formation Through the Oxidation of Reduced Oxidation State Phosphorus Compounds on the Hadean Earth	12
Understanding Functional Evolution in Orthologs and Paralogs	12
Phylogenetic and Evolutionary Analysis of Plant Small RNA 2′-O-Methyltransferase (HEN1) Protein Family	11
On the Nature of the Last Common Ancestor: A Story from its Translation Machinery	11
Evolution of Transcript Abundance is Influenced by Indels in Protein Low Complexity Regions	11

dN/dS-H, a New Test to Distinguish Different Selection Modes in Protein Evolution and Cancer Evolution	11
Systematic Detection of Alternative Open Reading Frames (altORFs) in Cancer Driver Genes	10
On Protein Loops, Prior Molecular States and Common Ancestors of Life	9
A Closer Look at Non-random Patterns Within Chemistry Space for a Smaller, Earlier Amino Acid Alphabet	9
Possible Acquisition and Molecular Evolution of vpu Genes Inferred from Comprehensive Sequence Analysis of Human and Simian Immunodeficiency Viruses	9
Molecular Footprints on Osmoregulation-Related Genes Associated with Freshwater Colonization by Cetaceans and Sirenians	9
Biochemical Property Based Positional Matrix: A New Approach Towards Genome Sequence Comparison	9
The De Novo Emergence of Two Brain Genes in the Human Lineage Appears to be Unsupported	8
Functional Diversity of the Lepidopteran ATP-Binding Cassette Transporters	8
Cystathionine Gamma-Lyase: A Potential Longevity Gene Under Selection?	8
Conservation of Protein Kinase A Substrates in the Cnidarian Coral Spermatozoa Among Animals and Their Molecular Evolution	8
Evolution of the Metazoan Protein Domain Repertoire Revealed by a Birth-Death-Gain Model	8
Understanding the Origin and Evolution of Tea (Camellia sinensis [L.]): Genomic Advances in Tea	8
RNA or DNA? Revisiting the Chemical Nature of the Cenancestral Genome	8
Reconstructing Evolutionary Histories with Hierarchical Orthologous Groups	8
Adaptation and Exaptation: From Small Molecules to Feathers	8
The Last Universal Common Ancestor of Ribosome-Encoding Organisms: Portrait of LUCA	8
Correction: Reconstructing Evolutionary Histories with Hierarchical Orthologous Groups	7
A New View of the Last Universal Common Ancestor	7
Biothermodynamics of Hemoglobin and Red Blood Cells: Analysis of Structure and Evolution of Hemoglobin and Red Blood Cells, Based on Molecular and Empirical Formulas, Biosynthesis Reactions, and Therm	7
EasyDIVER + : An Advanced Tool for Analyzing High Throughput Sequencing Data from In Vitro Evolution of Nucleic Acids or Amino Acids	7
GC Content Across Insect Genomes: Phylogenetic Patterns, Causes and Consequences	7
Evolution and Functional Diversification of Serine Racemase Homologs in Bacteria	7
Best Practices in Designing, Sequencing, and Identifying Random DNA Barcodes	7
Informatic Capabilities of Translation and Its Implications for the Origins of Life	7
Reduction of Tooth Replacement Disproportionately Affects the Evolution of Enamel Matrix Proteins	7
Codon Usage Evolution in Viruses: Implications for Survival and Pathogenicity	7
Correction: Sequence Divergence in Venom Genes Within and Between Montane Pitviper (Viperidae: Crotalinae: Cerrophidion) Species is Driven by Mutation–Drift Equilibrium	6
Caspase Domain Duplication During the Evolution of Caspase-16	6
Analysis of the MCTP Amino Acid Sequence Reveals the Conservation of Putative Calcium- and Lipid-Binding Pockets Within the C2 Domains In Silico	6
PAReTT: A Python Package for the Automated Retrieval and Management of Divergence Time Data from the TimeTree Resource for Downstream Analyses	6
FEZF2 and AIRE1: An Evolutionary Trade-off in the Elimination of Auto-reactive T Cells in the Thymus	6
A Law of Redundancy Compounds the Problem of Cancer and Precision Medicine	6
Promiscuous Domains in Eukaryotes and HAT Proteins in FUNGI Have Followed Different Evolutionary Paths	6
Deep Conservation and Unexpected Evolutionary History of Neighboring lncRNAs MALAT1 and NEAT1	6
Main Factors Shaping Amino Acid Usage Across Evolution	5
Evidence for Multiple Independent Expansions of Fox Gene Families Within Flatworms	5
Putative MutS2 Homologs in Algae: More Goods in Shopping Bag?	5
Selection Pressure Regulates the Evolution-Structure–Function Paradigm of Monocyte Chemoattractant Protein Family	5
APGW/AKH Precursor from Rotifer Brachionus plicatilis and the DNA Loss Model Explain Evolutionary Trends of the Neuropeptide LWamide, APGWamide, RPCH, AKH, ACP, CRZ, and GnRH Families	5
Origins and Functional Significance of Eukaryotic Protein Folds	5
OrthoGrafter: Rapid Identification of Orthologs from Precomputed Placement in Phylogenetic Trees	5
Is the Association of the Rare rs35667974 IFIH1 Gene Polymorphism With Autoimmune Diseases a Case of RNA Epigenetics?	5
The Mystery of Cancer Resistance: A Revelation Within Nature	5
Transposable Element Diversity Remains High in Gigantic Genomes	5
Evolutionary Nonindependence Between Human piRNAs and Their Potential Target Sites in Protein-Coding Genes	5
Correlated Evolution Drives Structural Convergence of Interacting Proteins	5
Correction: Principles of Molecular Evolution: Concepts from Non-equilibrium Thermodynamics for the Multilevel Theory of Learning	5
Co-evolution of alpha-helical transmembrane protein residues: large-scale variant profiling and complete mutational landscape of 2277 known PDB entries representing 504 unique human protein sequences	5
Tracking the Diversity and Chromosomal Distribution of the Olfactory Receptor Gene Repertoires of Three Anurans Species	5

Genomic AT Bias Coupled with Amino Acid Metabolism Modulates Codon Usage	4
2022 Zuckerkandl Prize	4
A Genomic Conceptualization of Species	4
Jump-Chain Simulation of Markov Substitution Processes Over Phylogenies	4
Context-Dependent Substitution Dynamics in Plastid DNA Across a Wide Range of Taxonomic Groups	4
Case Studies in the Assessment of Microbial Fitness: Seemingly Subtle Changes Can Have Major Effects on Phenotypic Outcomes	4
The Role of Selection and Migration in the Evolution of (Auto)Immunity Genes	3
Principles of Molecular Evolution: Concepts from Non-equilibrium Thermodynamics for the Multilevel Theory of Learning	3
Selection Across the Three-Dimensional Structure of Venom Proteins from North American Scolopendromorph Centipedes	3
Origin of Sex-Biased Mental Disorders: Do Males and Females Experience Different Selective Regimes?	3
Recurrent Independent Pseudogenization Events of the Sperm Fertilization Gene ZP3r in Apes and Monkeys	3
Convergent Evolution of Two Dopamine Receptor Genes: Repeated Evolution of Exon 6 Skipping in Drd2, and Repeated Deletion of Exon 6 in Drd3	3
Epistasis-Driven Evolution of the SARS-CoV-2 Secondary Structure	3
Introduction to the Special Issue on Early Evolution and the Last Common Ancestor	3
How Many Factors Influence Genomic GC Content Among Prokaryotes?	3
Quest for Orthologs in the era of Data Deluge and AI: Challenges and Innovations in Orthology Prediction and Data Integration	3
First Report on Presence of Mitochondrial Introns in Freshwater Sponges, and Pseudogenic Evidence of Their Loss	3
Molecular Evolution of Aryl Hydrocarbon Receptor Signaling Pathway Genes	3
Decay of Skin-Specific Gene Modules in Pangolins	3
A Simple Evolutionary Model of Genetic Robustness After Gene Duplication	3
The Unfinished Reconstructed Nature of the Last Universal Common Ancestor	3
Cost-Efficiency Optimization Serves as a Conserved Mechanism that Promotes Osteosarcoma in Mammals	3
Long-Term Adaptation to Galactose as a Sole Carbon Source Selects for Mutations Outside the Canonical GAL Pathway	3
Evolution of the Major Components of Innate Immunity in Animals	3
2024 Zuckerkandl Prize	3
Varying Modes of Selection Among Toxin Families in the Venoms of the Giant Desert Hairy Scorpions (Hadrurus)	3
Structural Analysis of Monomeric RNA-Dependent Polymerases Revisited	3
Collaborative Expression: Transcriptomics of Conus virgo Suggests Contribution of Multiple Secretory Glands to Venom Production	2
Expansion and Functional Diversification of Long-Wavelength-Sensitive Opsin in Anabantoid Fishes	2
Ancient Host-Virus Gene Transfer Hints at a Diverse Pre-LECA Virosphere	2
Analysis of Programmed Cell Death-1 (PD-1) Gene Variations (re11568821 and rs41386349) in HTLV-1 Infection Using One Primer Pair and Proviral Load	2
Nucleobases in Meteorites to Nucleobases in RNA and DNA?	2
Fit-Seq2.0: An Improved Software for High-Throughput Fitness Measurements Using Pooled Competition Assays	2
NCBI Orthologs: Public Resource and Scalable Method for Computing High-Precision Orthologs Across Eukaryotic Genomes	2
A Concept of Complementarity Between Complexity and Redundancy can Account for Kant’s Biological Teleology and Unify Mechanistic and Finalistic Biology	2
A Comparative Genomics Approach to Understanding the Evolution of Olfaction in Cetaceans	2
Human Riboviruses: A Comprehensive Study	2
Clay Minerals, Panacea or Parameter in RNA Oligomerization?	2
The Amphibian Major Histocompatibility Complex—A Review and Future Outlook	2
Conservation of a Chromosome 8 Inversion and Exon Mutations Confirm Common Gulonolactone Oxidase Gene Evolution Among Primates, Including H. Neanderthalensis	2
Positive Selection Shapes Breast Cancer Tumor Suppressor Genes: Unveiling Insights into BRCA1, BRCA2, and MDC1 Stability	2
Structural and Evolutionary Analysis of Proteins Endowed with a Nucleotidyltransferase, or Non-canonical Palm, Catalytic Domain	2
In Memoriam of Giorgio Bernardi and Noboru Sueoka: A Personal View	2
Extreme Sensitivity of Fitness to Environmental Conditions: Lessons from #1BigBatch	2
Revisiting the Design of the Long-Term Evolution Experiment with Escherichia coli	2
uORF-Mediated Translational Regulation of ATF4 Serves as an Evolutionarily Conserved Mechanism Contributing to Non-Small-Cell Lung Cancer (NSCLC) and Stress Response	2
The Abundance of Viroid-Like RNA Obelisk-S.s in Streptococcus sanguinis SK36 May Suffice for Evolutionary Persistence	2
Efficiency of Ancestral Inference and Characterization of Genetic Structure of Chinese Kazakh Group with a Novel InDel Panel	2
A Multi-level Perspective on the Evolution of Orthologs and Their Functions	2
Correction to: Evidence for Multiple Independent Expansions of Fox Gene Families Within Flatworms	2
Mutation Rate Variation and Other Challenges in 2-LTR Dating of Primate Endogenous Retrovirus Integrations	2
Profylo: A Python Package for Phylogenetic Profile Comparison and Analysis	2
Speciation Features of Ferdinandcohnia quinoae sp. nov to Adapt to the Plant Host	2
Exploring Flexibility and Folding Patterns Throughout Time in Voltage Sensors	2
The Hypervariable Tpr Multigene Family of Theileria Parasites, Defined by a Conserved, Membrane-Associated, C-Terminal Domain, Includes Several Copies with Defined Orthology Between Species	2
Functional Diversification and the Plant Secondary Cell Wall	2
Ancestral Information Analysis of Chinese Korean Ethnic Group via a Novel Multiplex DIP System	2
OrthoXML-Tools: A Toolkit for Manipulating OrthoXML Files for Orthology Data	2
Correction: G:U-Independent RNA Minihelix Aminoacylation by Nanoarchaeum equitans Alanyl-tRNA Synthetase: An Insight into the Evolution of Aminoacyl-tRNA Synthetases	2
On the Unknown Proteins of Eukaryotic Proteomes	2
Best Practices in Microbial Experimental Evolution	2